Fig. 2.

Overview of the PRISM web server. (a) The “Prism” tab is designed for online prediction. The “Predictions” tab is for browsing the accumulated data in the web server. The “Templates” tab is for browsing detailed information about the built-in template set. (b) For online prediction, two options are available: (1) predicting the interaction between two proteins (left panel) or (2) predicting interactions in a network (right panel). For the former option, the input is the PDB codes or PDB files of “Target 1” and “Target 2.” For the latter option, the input is the list of protein pairs with their PDB codes. The template code and e-mail address are optional inputs for both. (c) The “Results” page lists the predicted interactions with the target codes, the template (the column labeled “Interface”), and the calculated binding energy. Each interaction has a “View” button where an interactive visualization of the predicted complex is possible. Target 1 is colored blue and Target 2 is red. Their interface regions are in pink and light blue, respectively. The contacts in the interface region and the PDB file of the predicted complex are downloadable using the “Contact of Interface Residues” and “Structure” links, respectively